Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus

Background Duck plague virus (DPV), belonging to herpesviruses, is a linear double-stranded DNA virus. There are many reports about the outbreak of the duck plague in a variety of countries, which caused huge economic losses. Recently, increasing reports revealed that multiple long non-coding RNAs (lncRNAs) can possess great potential in the regulation of host antiviral immune response. Furthermore, it remains to be determined which specific molecular mechanisms are responsible for the DPV-host interaction in host immunity. Here, lncRNAs and mRNAs in DPV infected duck embryonic fibroblast (DEF) cells were identified by high-throughput RNA-sequencing (RNA-seq). And we predicted target genes of differentially expressed genes (DEGs) and formed a complex regulatory network depending on in-silico analysis and prediction. Result RNA-seq analysis results showed that 2921 lncRNAs were found at 30 h post-infection (hpi). In our study, 218 DE lncRNAs and 2840 DE mRNAs were obtained in DEF after DPV infection. Among these DEGs and target genes, some have been authenticated as immune-related molecules, such as a Macrophage mannose receptor (MR), Anas platyrhynchos toll-like receptor 2 (TLR2), leukocyte differentiation antigen, interleukin family, and their related regulatory factors. Furthermore, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis, we found that the target genes may have important effects on biological development, biosynthesis, signal transduction, cell biological regulation, and cell process. Also, we obtained, the potential targeting relationship existing in DEF cells between host lncRNAs and DPV-encoded miRNAs by software. Conclusions This study revealed not only expression changes, but also the possible biological regulatory relationship of lncRNAs and mRNAs in DPV infected DEF cells. Together, these data and analyses provide additional insight into the role of lncRNAs and mRNAs in the host's immune response to DPV infection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08739-7.

waterfowl migrate, the disease can spread widely inside and between continents around the world, causing huge economic losses [3][4][5][6]. After DPV infection, the main injured organs in the disease seem to be the brain, liver, kidney, and lung, and the main pathological features are bleeding, inflammation, and necrosis of tissues, and organs [1,7]. In China, the duck plague was first reported in 1959 and verified in many regions of China. And now the duck plague has not been wholly conquered in China, and there are still reports once in a while [8].
The definition of Long non-coding RNAs (lncRNAs) is non-protein-coding transcripts with more than 200 nucleotides, mainly classified into antisense lncRNAs, sense RNAs, bidirectional lncRNAs, large intergenic non-coding RNAs (lincRNAs), and intronic transcript [9,10]. It has been found that lncRNAs have a variety of functions, including epigenetic regulation, transcriptional regulation, and post-transcriptional regulation, and unexpectedly, some transcripts annotated as lncR-NAs can encode small proteins [10][11][12]. In addition, with the deepening of research, more researchers have started to pay more attention to that lncRNAs can also participate in the interaction between virus and host. The lnc-zc3h7a existed in mouse macrophage RAW264.7, can be used as a scaffold to stabilize retinoid acid-inducible gene I (RIG-I) -Tripartite Motif Containing 25 (TRIM25) complex and promote TRIM25-mediated ubiquitination of RIG-I, finally to participate in type I interferon (IFN) signal transduction and regulate RNA virus replication both in vivo and in vitro [13]. Similarly, MALAT1 can bind to TAR DNA-binding protein 43 (TDP43) in resting macrophages and inhibit IFNs expression induced by interferon regulatory Factor 3 (IRF3) [14]. In addition, there is a unique mechanism by which the virus absorbs host lncRNA to assist virus replication. After hepatitis C virus (HCV) infection, lncRNA EGOT was found to be significantly up-regulated. And Previous studies showed that EGOT had a highly significant negative correlation with innate immune-related genes that may block the antiviral response to promote virus replication [15].
Currently, there are increasing studies on lncRNAs related to avian diseases, such as the H5N1 influenza virus [16], duck enteritis salmonella [17], and duck Tembusu virus (DTMUV) [18]. However, there is a lack of reports on host lncRNAs expression induced by DPV infection. To solve this problem, the transcriptome of DPV infected duck embryonic fibroblasts (DEF) was sequenced by RNA-seq. Here we identified the differentially expressed (DE) lncRNAs and mRNAs compared with the infected and uninfected DEF cells, and predicted the target genes of DE lncRNAs using bioinformatics analysis. Based on the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified that differentially expressed genes (DEGs) in DEF cells were significantly associated with the biological processes and signal pathways.

Characterization of DPV infection in DEFs
At a multiplicity of infection (MOI) of 1.0, duck embryonic fibroblasts (DEF) cells were infected with DPV. In our study, CPE was observed in DPV-infected DEFs after 24 hpi, and DPV propagation in DEF cell culture began to slow down at 30 hpi (Fig. 1a, b), similar to previous studies [19,20]. As a result, 30 hpi and an MOI of 1.0 were chosen as the condition for preparing cell samples for future high-throughput RNA-sequencing (RNA-seq).

LncRNAs screening
After a series of data sorting and filtering processes, the number of high-quality reads per each sample is about 66,715,946-77,362,586 (Additional file 1: Table S1 and Additional file 2: Table S2). The filtered data were aligned to the reference genome. The percentage of the total aligned reads in the control group was more than 90%, while in the infection group it was more than 70% (Additional file 3: Table S3). We screened lncRNAs in the assembled transcript set [10,21,22]: (1) Screening the transcripts with length > = 200 bp and exon number > = 2; (2) Screening the transcripts with Class x/u/i (Anti-sense lncRNA/Intergenic lncRNA/Intronic lncRNA); (3) Screening for transcripts with coverage > 3 in at least one sample. That is, it appeared at least three times in one sample's transcripts.
A total of 61,391 long transcripts were screened out in the first step, 5994 long transcripts were screened out in the second step, and finally, 5941 long transcripts were screened out for follow-up analysis (Fig. 2a). Further analysis of the coding potential of the candidate lncRNAs was performed to get high-credibility lncRNAs. A total of 2921 novel lncRNAs with high-reliability were found by the following three methods: plek, CNCI, and pfamscan ( Fig. 2a, b).

Comparative analysis of lncRNAs and mRNAs
The structures of known and unknown lncRNAs and mRNAs were compared. On the one hand, the result showed the molecular differences between lncRNAs and mRNAs, on the other hand, it verified whether the predicted lncRNAs accord with the general characteristics. As shown in Fig. 2, the results showed that on the whole, the number of mRNA transcripts was widely distributed, ranging from 1 to 10, mainly in the range of 1-2, whereas the number of lncRNAs transcripts was only in the range of 1-6, and mainly a single transcript (Fig. 3a).
In terms of length analysis, the major length of mRNAs was in the range of > = 5000 and 800-1600, while lncR-NAs were chiefly distributed in the range of 200-300 and showed a stepwise downward trend in the range of 400-4800, but there was a certain quantitative trend rising in the range of > = 5000 (Fig. 3b). Most mRNAs contained   Fig. 3c). Based on the results of FPKM (fragments per kilobases per million fragments) density distribution, we observed that the FPKM distribution of mRNAs was gathered at 1-2, while the expression level of lncRNA is lower (Fig. 3d, e).

Deep sequencing results
We also performed PCA (Principal Component Analysis) to check the correlation between samples. And it was found that there were greater differences in the total lncRNAs of biological repeat samples in each treatment group, compared with mRNAs ( Fig. 4a, b).
The calculation method of P value of DESeq2 is very strict. Therefore, we choose |log2 fold change (infected/ mock in expression) |> 1 and p-value < 0.05 as the screening standard, hoping to get more DEGs for analysis. The differential expression analysis results indicated that compared with the control group (Fig. 4c), we identified 2840 DE mRNAs in DEF after DPV infection, of which 1386 were up-regulated and 1454 were down-regulated (Additional file 4: Table S4), and 218 DE lncRNAs, of which 169 were up-regulated and 49 were down-regulated (Additional file 5: Table S5 and Additional file 6: Table S6). Besides, we used volcano plots and heat maps to show DE lncRNAs and DE mRNAs ( Fig. 5a-d).
Among them, the mRNA with the most significant difference in expression level are actin and myosin-related factors. Further, some DE mRNAs have been identified as immune-related molecules, which can be classified into the following three categories: pattern recognition receptors (PRRs) (such as Macrophage mannose receptor 1 and Anas platyrhynchos toll-like receptor 2), leukocyte differentiation antigens (like CD81, CD82, CD36, and CD2 associated protein) and immune cell-derived cytokines and their related regulatory factors (such as interleukin 15, interleukin 21 receptor, interleukin 6 family cytokine, interleukin 23 receptor, interleukin-9 receptor-like gene, interleukin 18 receptor accessory protein, interleukin 19, interleukin 6 signal transducer, cytokineinducible SH2 containing protein, and Cytokine-like 1  Table S4).

Potential interacting genes prediction
Then, we predicted potential interacting genes of lncRNA in cis-and trans-regulation, as shown in figures ( Fig. 6 and Fig. 7). The previous study has shown that lncRNA can regulate the expression of adjacent genes by recruiting regulatory factors and competing for TF (Transcription Factor) and Pol ll (RNA polymerase II) required for transcription. Or the transcription of lncRNA can interfere with the cis-regulatory element of mRNA, contained in the lncRNA encoded region [10]. Besides, lncRNAs can also regulate chromatin state and structure, organization of nuclear, and trans-acting factors to regulate distal gene expression [10]. And it was found that in the predicted results, 3762 lncRNAs (of a total 3814) were predicted to have cis regulatory function, and1388 lncRNAs could act in trans-regulation. Interestingly, 1262 lncR-NAs have a large number of possible associated genes, whether in cis-regulation or trans-regulation (Additional file 7: Table S7 and Additional file 8: Table S8).
At the same time, KEGG analysis showed that multiple signal pathways associated with inflammation  Table S10 and Additional file 12:  Table S12), for instance, Toll-like receptor signaling pathway, C-type lectin receptor signaling pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway were found in both trans-and cis-regulation. Also, the mitogen-activated protein kinase (MAPK) signaling pathway and Cytokine-cytokine receptor interaction were enriched at cis-regulation.
The results of KEGG pathway analyses revealed that the enrichment results were significantly related to (p < 0.05) the signal transduction, metabolism, and biomembrane (Additional file 14: Table S14). And the top enriched KEGG pathway was MAPK signaling pathway (p < 0.05). Similar to the enrichment results of lncRNA predicted target genes, Cytokine-cytokine receptor interaction, Wnt signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, and RIG-I-like receptor signaling pathway were all present in the KEGG pathway analyses.

Establishment of predicted competitive endogenous RNA (ceRNA) network
LncRNA-miRNA plays a significant role in gene expression regulation. LncRNA with microRNA response elements (MREs) can be used as a competing endogenous RNA (ceRNA) to inactivate miRNA by binding to miRNA [23]. Because most lncRNAs are structurally similar to mRNAs, miRNA may also negatively regulate the expression of lncRNA through a similar mechanism of action on mRNA, and then plays a series of biological roles [24]. At the same time, miRNA can also promote the expression of specific lncRNA [25]. In this study, we obtained the prediction results of the interaction between DE lncRNAs and miRNAs encoded by DPV virus [26]. And we found that each miRNA was predicted to interact with a large number of lncRNAs, and many lncRNAs could also be targeted by multiple miRNAs at the same time (Additional Fig. 6 Prediction of potential cis-target genes of lncRNAs. In the chart, we use blue to represent lncRNA, red to represent mRNA, and wiring to represent target relationship by the Igraph package (https:// igraph. org/) file 15: Table S15 and Additional file 16: Figure S1), for instance, 24 viral miRNAs were all predicted to target ENSAPLT00020019865.

Validation of DE lncRNAs and mRNAs by qRT-PCR
To validate the DEGs in RNA-seq results, we randomly selected 12 DEGs (6 lncRNAs and 6 mRNAs) for qRT-PCR analysis. And it was found that among the 6 lncRNAs, there were 5 up-regulated lncRNAs and 1 down-regulated lncRNA (MSTRG.24727.2) by qRT-PCR analysis, differential expression patterns of which were consistent with RNA-seq results (Additional file 17: Figure S2). Similarly, the expression trend of the chosen mRNAs was in accordance with the results of RNA-seq analysis (Additional file 18: Figure S3).

Discussion
With an in-depth understanding of lncRNA, it has been found that virus infection can affect the expression of host lncRNAs, and lncRNAs can also play a unique role in the process of virus infection. For example, RIG-Idependent IAV upregulated noncoding RNA (RDUR), induced by Influenza A virus (IAV) infection, can positively regulate the signal transduction of type I interferon (IFN-1) by affecting IRF3 and further upregulates the expression of several vital antiviral molecules. It is concluded that RDUR is a critical regulator of innate immunity against viral infection [27]. And lncRNA-GM can bind to glutathione S-transferase M1 (GSTM1), block the interaction between GSTM1 and TANK binding kinase 1 (TBK1), and reduce GSTM1-mediated glutathione. Finally, the deficiency of lncRNA-GM in mice Fig. 7 Prediction of potential trans-target genes of lncRNAs. In the chart, we use blue to represent lncRNA, red to represent mRNA, and wiring to represent target relationship by the Igraph package (https:// igraph. org/) increases sensitivity to viral infection and interferes with the production of IFN-I [28]. There are also lncRNA-ACOD1, which are effectively induced by several viruses. This lncRNA can promote viral replication by activating the glutamic acid transaminase 2 (GOT2), a metabolic enzyme. Interestingly, the enhancement of GOT2 activity by lncRNA-ACOD1 is necessary for virus replication [29]. DPV is a pathogen causing a hot, acute, and septic infectious disease in ducks, geese, and swans, with a great number of economic losses [1]. Moreover, the regulatory mechanism between DPV and host remains to be discussed. Here we analyzed the transcriptome of DPV In our study, we found that some DE mRNAs were closely related to immune regulation, such as toll-like receptor 2 (TLR2), mannose receptor (MR) family, T cell surface antigen, interleukin family, and their related regulatory factors. There are many reports showed that the above factors are involved in the regulation of the host antiviral immune response. For example, the coordinated activation of TLR2 and TLR9 in trigeminal ganglion exists in the defence response of mice to the herpes simplex virus-1 (HSV-1), while the expression of TLRs in HSV-1 infected mice is significantly increased [30]. And it has been reported that innate immune recognition of vaccinia virus (VV) is mediated by TLR2 [31]. However, it is also reported that the above immune factors can participate in the interaction between the virus and the host. For example, macrophage mannose receptor (MMR) can participate in the infection of mouse macrophages by influenza virus, which is necessary for endocytic uptake of virus [32]. Similarly, CD81 can promote the entry of the HCV into host cells [33], and CD2 related protein (CD2AP) can promote the assembly of HCV [34]. Meanwhile, the differential expression level of actin-related factors changed significantly. Actin is abundant in eukaryotic cells and previous studies have shown that actin could intimately interact with lentiviruses [35]. Also, cofilin, one of the actin-binding proteins, was found to be involved in the process of HSV infection [36]. The findings suggested that DE mRNAs may similarly regulate the pathogenicity of DPV.
In addition, the functional analysis indicated that the target genes and DEGs significantly related to (p < 0.05) biological development, biosynthesis, metabolism, and signal transduction. At the same time, some targets were enriched in IL-2 terms, Wnt signaling pathway, JAK/STAT pathway terms, and other important GO terms. Interleukin-2 (IL-2) is a growth factor of various cells, which is closely related to the growth and differentiation of T cells, the development of functional B cells, and the activation of NK cells [37]. Studies have proved that duck IL-2 is an important immunomodulatory molecule, which has been fully verified in chickens and mammals [38]. Similarly, JAK/STAT pathway is an important cytokine signal transduction pathway, which is activated by a variety of cytokines, growth factors, and receptors. And it involves many biological processes such as immune regulation, inflammatory response, cell proliferation, differentiation, apoptosis, angiogenesis, oxidative stress, and tumor formation [39]. Also, it is related to the process of a variety of viruses infection, such as porcine deltacoronavirus (PDCoV) [40], hepatitis B virus (HBV) [41]. And the Wnt pathway is an important signal pathway, which participates in the regulation of a variety of cell processes, which is closely related to the development of the body, the maintenance of homeostasis, and the occurrence and development of a variety of diseases, including viral diseases [42][43][44]. Therefore, the above results indicated that there may be IL-2, Wnt pathway or JAK/STAT pathway-dependent manners in DEF after DPV infection to deal with virus infection. In addition, after the KEGG pathway enrichment analysis, we also found target genes were significantly enriched in MAPK signaling pathway (p < 0.05), RIG-I-like receptor signaling pathway, Toll-like receptor signaling pathway, and other immune-related pathways. It has been reported that MAPK pathway activation is important for the replication of many viruses, such as foot-andmouth disease virus (FMDV) [45], bovine herpesvirus type 1 (BoHV-1) [46,47], and KS associated herpesvirus (KSHV) [48]. Perhaps there is a similar mechanism in DPV infected DEF cells. Further, both RIG-I and TLR can participate in NF-κB signal transduction after detecting viruses to regulate host antiviral immunity [49,50]. This is also consistent with the enrichment of NF-κB signaling pathway-related GO terms (GO:0,043,124, p < 0.05) in the functional analysis of DEGs.
In addition, we also analyzed the potential viral miR-NAs that may interact with DE lncRNAs based on the DPV-encoded miRNA sequence spectrum of Wu et al. [26]. Previous studies have also shown that viral miR-NAs can also play an important role in virus invasion and replication process [51][52][53], and that lncRNA could post-transcriptionally regulate target genes by micro-RNA response elements (MREs) [23]. Here, we would like to further understand whether DE lncRNAs may be involved in a similar process during DPV infection. However, these analysis results need further experimental exploration to prove.

Conclusion
In our study, we screened out numerous DE lncRNAs and mRNAs by RNA-seq, formed a potential target interaction network in silico analysis, and predicted potential biological functions. LncRNA continues to be hot in the field of scientific research in recent years because of its various gene regulation mechanisms and a wide range of biological functions. We obtained a total of 218 DE lncRNAs and 2840 DE mRNAs, which were beneficial to understand the cellular mechanism of DPV infection with DEF.

Cell and virus
Primary DEF cells were obtained from 9-day-old duck embryos after trypsin digestion for subsequent experiments and cultured in Dulbecco's modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (Gibco, USA) at 37 °C with 5% CO2. The DPV CHv (GenBank accession No. JQ647509) used in this study was kept in our laboratory. At a multiplicity of infection (MOI) of 1.0, duck embryonic fibroblasts (DEF) cells were infected with DPV or mock-infected with DMEM as control.

RNA isolation and RNA-Seq
All experiments were carried out in triplicate. At 30 h post-infection (hpi) [19,20], total cellular RNAs were extracted using the RNAiso plus reagent (TaKaRa, Japan). The purity, integrity, and concentration of total RNA samples were evaluated and tested by NanoDrop NC2000 Spectrophotometer (Thermo Fisher Scientific, USA) and Agilent RNA 6000 nano kit (Agilent Technologies, USA). Rin value (RNA integrity number) was automatically generated by Agilent 2100 Bioanalyzer (Agilent Technologies, USA) which represents the quantitative value of RNA integrity. The quality test results showed that the RIN values of the samples were 10, which met the requirements of database construction and sequencing. All the infected and uninfected samples were sequenced by Shanghai Personal Biotechnology (Shanghai, China).

Identification of differentially expressed RNAs
The correlation of gene expression level between biological repeat samples is an important index to test the reliability of experiments and the rationality of sample selection. We used DESeq Software package(http:// www. bioco nduct or. org/ packa ges/ relea se/ bioc/ html/ DESeq. html) to carry out PCA (principal component analysis) for each sample according to the expression amount [59,60]. Then, we used HTSeq statistics (https:// htseq. readt hedocs. io/ en/ master/) to obtain the reads count on each gene as the original expression level [61]. In order to facilitate comparison of gene expression of different genes in different samples, we used FPKM (fragments per kilobases per million fragments) as the standard of measurement by the Cufflinks program (http:// cole-trapn ell-lab. github. io/ cuffl inks/) [62]. We also used Stringtie software to obtain the reads count of lncRNAs and then homogenized the expression level with FPKM. The differential expression analyses of RNAs were performed by DESeq (http:// www. bioco nduct or. org/ packa ges/ relea se/ bioc/ html/ DESeq. html) [59,60]. The conditions for screening DEGs were as follows: |log2 fold change (infected/mock in expression) |> 1 and p-value < 0.05. We used the phatmap software package (https:// CRAN.Rproje ct. org/ packa ge= pheat map) to conduct a two-way cluster analysis on the Union and samples of different genes in all comparison groups. According to the expression level of the same genes in different samples and the expression patterns of different genes in the same sample, the Euclidean method was used to calculate the distance, and the hierarchical clustering longest distance method (complete linkage) was used for clustering.

Target genes prediction of lncRNAs
Increasing researches showed that the cis-regulatory function of lncRNAs is associated with the proteincoding genes near their genomic locations [10,19,63]. Therefore, to explore the regulatory function of lncR-NAs, the protein-coding genes within 100 kb upstream and downstream of the lncRNA genes were searched and thought to be the cis-regulatory target genes of their corresponding lncRNAs.
In contrast, the basic principle of trans-regulatory target genes prediction holds that the function of lncRNA is dependent on its co-expressed protein-coding genes [10,19,63]. The conditions of correlation coefficient | correlation |> 0.95 and p-value < 0.05 were used to screen the trans-regulatory relationship between lncRNAs and mRNAs.

In-silico gene functional prediction analysis
We used the TopGO (http:// www. bioco nduct or. org/ packa ges/ relea se/ bioc/ html/ RamiGO. html) for GO enrichment analysis of DEGs and target genes [64]. Based on the DEGs and target genes annotated by the GO database (http:// geneo ntolo gy. org/), then we calculated the p-value of DEGs and target genes by hypergeometric distribution method (p-value < 0.05 is regarded as the standard of significant enrichment), and took the whole genome as the background to screen the GO terms with significant enrichment of DEGs and target genes, to determine the main biological functions performed by DEGs and target genes [65]. Furthermore, we predicted the associated pathways of DEGs and target genes by the KEGG database (http:// www. kegg. jp/) [66,67]. Similarly, the criterion for significant enrichment is p-value < 0.05.

QRT -PCR Analysis
We randomly selected several DEGs and determined the expression changes by Quantitative Real-time PCR (qRT-PCR) to verify the validity of sequencing data. The extracted total RNA was used to reverse transcribed to cDNA by PrimeScript ™ RT reagent Kit with gDNA Eraser (Perfect Real Time) (TaKaRa, Japan). The expression of DEGs was detected by the CFX Connect real-Time PCR Detection System (Bio-Rad, USA) and TB Green ® Premix Ex Taq ™ II(Tli RNaseH Plus) (TaKaRa, Japan). The β-actin gene was used to standardize the expression of DEGs, and calculate relative expression levels by the 2-△△Ct method [70]. The primers used in this study were synthesized by Huada Company (Guangdong, China) and shown in Table 1.